Hi,
As you can see in the old Developers Guide:
http://devnet.kentico.com/docs/5_5/devguide/index.html?system_requirements.htm IE9 is not officially supported for content editing in v5.5. The reason is that the IE9 was released after Kentico v5.5.
Anyway, I've tested and there is no problem while working with FCKEditor in IE9. I would recommend you to check your JavaScripts because it is possible they are in conflict with FCKEditor functionality. Try to remove them one by one a maybe you will the reason of this issue.
On the other side, I would still recommend you to apply at least the latest hotfix (shouldn't affect your customization) and eventually upgrade to v6. Please understand that you are in the specific state and we had already fixed many issues in the hotfixes, especially about bugs, security updates and improved functionality.
Best regards,
Martin Danko